Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done - so any tips would be greatly appreciated.

Many thanks
Eli